Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Introduction

Start here if you are new to RNA-Seq analysis in Galaxy

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Transcriptomics
Reference-based RNA-Seq data analysis
De novo transcriptome reconstruction with RNA-Seq

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Lesson Slides Hands-on Recordings Input dataset Workflows
1: RNA-Seq reads to counts
2: RNA-seq counts to genes
3: RNA-seq genes to pathways

Visualisation

Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
RNA Seq Counts to Viz in R
Visualization of RNA-Seq results with CummeRbund
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with Volcano Plot in R
Visualization of RNA-Seq results with heatmap2
Pathway analysis with the MINERVA Platform

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
CLIP-Seq data analysis from pre-processing to motif detection
Differential abundance testing of small RNAs
GO Enrichment Analysis
Genome-wide alternative splicing analysis
Network analysis with Heinz
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
RNA-seq Alignment with STAR
Small Non-coding RNA Clustering using BlockClust
Whole transcriptome analysis of Arabidopsis thaliana

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Community Resources

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoMaria Doyle avatar Maria Doyleorcid logoFlorian Heyl avatar Florian Heyl

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

orcid logoPavankumar Videm avatar Pavankumar VidemCasper de Visser avatar Casper de VisserMarkus Wolfien avatar Markus Wolfienorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoBérénice Batut avatar Bérénice Batutorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoFlorian Heyl avatar Florian HeylJames Taylor avatar James Taylororcid logoCristóbal Gallardo avatar Cristóbal GallardoBelinda Phipson avatar Belinda Phipsonorcid logoMaria Doyle avatar Maria Doyleorcid logoArmin Dadras avatar Armin Dadrasorcid logoClea Siguret avatar Clea Siguretorcid logoBjörn Grüning avatar Björn GrüningOlivier Dameron avatar Olivier DameronNiall Beard avatar Niall BeardShian Su avatar Shian Suorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoPeter van Heusden avatar Peter van HeusdenCharlotte Adang avatar Charlotte AdangChao Zhang avatar Chao ZhangGildas Le Corguillé avatar Gildas Le Corguilléorcid logoLinelle Abueg avatar Linelle Abuegorcid logoErwan Corre avatar Erwan Correorcid logoMo Heydarian avatar Mo Heydarianorcid logoIacopo Cristoferi avatar Iacopo Cristoferiorcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solanoorcid logoMyrthe van Baardwijk avatar Myrthe van Baardwijkorcid logoMatti Hoch avatar Matti HochJovana Maksimovic avatar Jovana Maksimovicorcid logoMarek Ostaszewski avatar Marek Ostaszewskiorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoToby Hodges avatar Toby Hodgesorcid logoNicola Soranzo avatar Nicola SoranzoJosé Manuel Domínguez avatar José Manuel DomínguezMatt Ritchie avatar Matt RitchieSimon Bray avatar Simon BrayEkaterina Polkh avatar Ekaterina PolkhCharity Law avatar Charity Laworcid logoMallory Freeberg avatar Mallory Freebergorcid logoClemens Blank avatar Clemens BlankDaniel Maticzka avatar Daniel Maticzkaorcid logoMartin Čech avatar Martin Čechorcid logoAnne Fouilloux avatar Anne FouillouxMateusz Kuzak avatar Mateusz KuzakAnne Siegel avatar Anne SiegelXavier Garnier avatar Xavier Garnierorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzAnton Nekrutenko avatar Anton NekrutenkoAnna Trigos avatar Anna TrigosHarriet Dashnow avatar Harriet DashnowSanjay Kumar Srikakulam avatar Sanjay Kumar Srikakulamorcid logoHelena Rasche avatar Helena RascheMehmet Tekman avatar Mehmet Tekmanorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoGraeme Tyson avatar Graeme Tysonorcid logoMateo Boudet avatar Mateo BoudetPeter-Bram 't Hoen avatar Peter-Bram 't HoenIGC Bioinformatics Unit avatar IGC Bioinformatics UnitXi Liu avatar Xi Liuorcid logoMira Kuntz avatar Mira Kuntzorcid logoLucille Delisle avatar Lucille DelisleMarius van den Beek avatar Marius van den Beekorcid logoTeresa Müller avatar Teresa MüllerAndrea Bagnacani avatar Andrea BagnacaniWilliam Durand avatar William Durand

Funding

These individuals or organisations provided funding support for the development of this resource

References